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Yoshihara M, Coschiera A, Bachmann JA, Pucci M, Li H, Bhagat S, Murakawa Y, Weltner J, Jouhilahti EM, Swoboda P, Sahlén P, Kere J. Transcriptional enhancers in human neuronal differentiation provide clues to neuronal disorders. EMBO Rep 2025; 26:1212-1237. [PMID: 39948187 PMCID: PMC11893885 DOI: 10.1038/s44319-025-00372-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 12/28/2024] [Accepted: 01/09/2025] [Indexed: 03/12/2025] Open
Abstract
Genome-wide association studies (GWASs) have identified thousands of variants associated with complex phenotypes, including neuropsychiatric disorders. To better understand their pathogenesis, it is necessary to identify the functional roles of these variants, which are largely located in non-coding DNA regions. Here, we employ a human mesencephalic neuronal cell differentiation model, LUHMES, with sensitive and high-resolution methods to discover enhancers (NET-CAGE), perform DNA conformation analysis (Capture Hi-C) to link enhancers to their target genes, and finally validate selected interactions. We expand the number of known enhancers active in differentiating human LUHMES neurons to 47,350, and find overlap with GWAS variants for Parkinson's disease and schizophrenia. Our findings reveal a fine-tuned regulation of human neuronal differentiation, even between adjacent developmental stages; provide a valuable resource for further studies on neuronal development, regulation, and disorders; and emphasize the importance of exploring the vast regulatory potential of non-coding DNA and enhancers.
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Affiliation(s)
- Masahito Yoshihara
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden
- Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita, Osaka, Japan
| | - Andrea Coschiera
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden
| | - Jörg A Bachmann
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mariangela Pucci
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden
| | - Shruti Bhagat
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jere Weltner
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Folkhälsan Research Centre, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden.
| | - Pelin Sahlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
| | - Juha Kere
- Department of Medicine Huddinge (MedH), Biosciences and Nutrition Unit, Karolinska Institutet, Stockholm, Sweden.
- Folkhälsan Research Centre, Helsinki, Finland.
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.
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Hjort L, Bredgaard SS, Manitta E, Marques I, Sørensen AE, Martino D, Grunnet LG, Kelstrup L, Houshmand-Oeregaard A, Clausen TD, Mathiesen ER, Olsen SF, Saffery R, Barrès R, Damm P, Vaag AA, Dalgaard LT. Epigenetics of the non-coding RNA nc886 across blood, adipose tissue and skeletal muscle in offspring exposed to diabetes in pregnancy. Clin Epigenetics 2024; 16:61. [PMID: 38715048 PMCID: PMC11077860 DOI: 10.1186/s13148-024-01673-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/20/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Diabetes in pregnancy is associated with increased risk of long-term metabolic disease in the offspring, potentially mediated by in utero epigenetic variation. Previously, we identified multiple differentially methylated single CpG sites in offspring of women with gestational diabetes mellitus (GDM), but whether stretches of differentially methylated regions (DMRs) can also be identified in adolescent GDM offspring is unknown. Here, we investigate which DNA regions in adolescent offspring are differentially methylated in blood by exposure to diabetes in pregnancy. The secondary aim was to characterize the RNA expression of the identified DMR, which contained the nc886 non-coding RNA. METHODS To identify DMRs, we employed the bump hunter method in samples from young (9-16 yr, n = 92) offspring of women with GDM (O-GDM) and control offspring (n = 94). Validation by pyrosequencing was performed in an adult offspring cohort (age 28-33 years) consisting of O-GDM (n = 82), offspring exposed to maternal type 1 diabetes (O-T1D, n = 67) and control offspring (O-BP, n = 57). RNA-expression was measured using RT-qPCR in subcutaneous adipose tissue and skeletal muscle. RESULTS One significant DMR represented by 10 CpGs with a bimodal methylation pattern was identified, located in the nc886/VTRNA2-1 non-coding RNA gene. Low methylation status across all CpGs of the nc886 in the young offspring was associated with maternal GDM. While low methylation degree in adult offspring in blood, adipose tissue, and skeletal muscle was not associated with maternal GDM, adipose tissue nc886 expression was increased in O-GDM compared to O-BP, but not in O-T1D. In addition, adipose tissue nc886 expression levels were positively associated with maternal pre-pregnancy BMI (p = 0.006), but not with the offspring's own adiposity. CONCLUSIONS Our results highlight that nc886 is a metastable epiallele, whose methylation in young offspring is negatively correlated with maternal obesity and GDM status. The physiological effect of nc886 may be more important in adipose tissue than in skeletal muscle. Further research should aim to investigate how nc886 regulation in adipose tissue by exposure to GDM may contribute to development of metabolic disease.
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Affiliation(s)
- Line Hjort
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark.
| | | | - Eleonora Manitta
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irene Marques
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | | | - David Martino
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
| | - Louise Groth Grunnet
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
| | - Louise Kelstrup
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Gynecology and Obstetrics, Herlev Hospital, Herlev, Denmark
| | - Azadeh Houshmand-Oeregaard
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk A/S, Bagsværd, Denmark
| | - Tine Dalsgaard Clausen
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Reinhardt Mathiesen
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | | | - Richard Saffery
- Murdoch Children's Research Institute, Parkville, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Damm
- Center for Pregnant Women With Diabetes, Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Allan Arthur Vaag
- Clinical Research, Steno Diabetes Center Copenhagen, Herlev Hospital, Herlev, Denmark
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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McAllan L, Baranasic D, Villicaña S, Brown S, Zhang W, Lehne B, Adamo M, Jenkinson A, Elkalaawy M, Mohammadi B, Hashemi M, Fernandes N, Lambie N, Williams R, Christiansen C, Yang Y, Zudina L, Lagou V, Tan S, Castillo-Fernandez J, King JWD, Soong R, Elliott P, Scott J, Prokopenko I, Cebola I, Loh M, Lenhard B, Batterham RL, Bell JT, Chambers JC, Kooner JS, Scott WR. Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. Nat Commun 2023; 14:2784. [PMID: 37188674 PMCID: PMC10185556 DOI: 10.1038/s41467-023-38439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.
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Affiliation(s)
- Liam McAllan
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Scarlett Brown
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Marco Adamo
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Andrew Jenkinson
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Mohamed Elkalaawy
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Borzoueh Mohammadi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Majid Hashemi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathalie Lambie
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Richard Williams
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Youwen Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- School of Cardiovascular and Metabolic Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Liudmila Zudina
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
| | - Vasiliki Lagou
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Sili Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - James W D King
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Institute for Health Research Biomedical Research Centre, Imperial College London, London, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Rachel L Batterham
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College, London, WC1E 6JJ, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, W1T 7DN, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - William R Scott
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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Atic AI, Thiele M, Munk A, Dalgaard LT. Circulating miRNAs associated with nonalcoholic fatty liver disease. Am J Physiol Cell Physiol 2023; 324:C588-C602. [PMID: 36645666 DOI: 10.1152/ajpcell.00253.2022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRNAs) are secreted from cells as either protein-bound or enclosed in extracellular vesicles. Circulating liver-derived miRNAs are modifiable by weight-loss or insulin-sensitizing treatments, indicating that they could be important biomarker candidates for diagnosis, monitoring, and prognosis in nonalcoholic liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Unfortunately, the noninvasive diagnosis of NASH and fibrosis remains a key challenge, which limits case finding. Current diagnostic guidelines, therefore, recommend liver biopsies, with risks of pain and bleeding for the patient and substantial healthcare costs. Here, we summarize mechanisms of RNA secretion and review circulating RNAs associated with NAFLD and NASH for their biomarker potential. Few circulating miRNAs are consistently associated with NAFLD/NASH: miR-122, miR-21, miR-34a, miR-192, miR-193, and the miR-17-92 miRNA-cluster. The hepatocyte-enriched miRNA-122 is consistently increased in NAFLD and NASH but decreased in liver cirrhosis. Circulating miR-34a, part of an existing diagnostic algorithm for NAFLD, and miR-21 are consistently increased in NAFLD and NASH. MiR-192 appears to be prominently upregulated in NASH compared with NAFDL, whereas miR-193 was reported to distinguish NASH from fibrosis. Various members of miRNA cluster miR-17-92 are reported to be associated with NAFLD and NASH, although with less consistency. Several other circulating miRNAs have been reported to be associated with fatty liver in a few studies, indicating the existence of more circulating miRNAs with relevant as diagnostic markers for NAFLD or NASH. Thus, circulating miRNAs show potential as biomarkers of fatty liver disease, but more information about phenotype specificity and longitudinal regulation is needed.
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Affiliation(s)
- Amila Iriskic Atic
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Novo Nordisk A/S, Obesity Research, Måløv, Denmark
| | - Maja Thiele
- Department of Gastroenterology and Hepatology, Center for Liver Research, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
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5
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Chicco D, Jurman G. A brief survey of tools for genomic regions enrichment analysis. FRONTIERS IN BIOINFORMATICS 2022; 2:968327. [PMID: 36388843 PMCID: PMC9645122 DOI: 10.3389/fbinf.2022.968327] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Functional enrichment analysis or pathway enrichment analysis (PEA) is a bioinformatics technique which identifies the most over-represented biological pathways in a list of genes compared to those that would be associated with them by chance. These biological functions are found on bioinformatics annotated databases such as The Gene Ontology or KEGG; the more abundant pathways are identified through statistical techniques such as Fisher’s exact test. All PEA tools require a list of genes as input. A few tools, however, read lists of genomic regions as input rather than lists of genes, and first associate these chromosome regions with their corresponding genes. These tools perform a procedure called genomic regions enrichment analysis, which can be useful for detecting the biological pathways related to a set of chromosome regions. In this brief survey, we analyze six tools for genomic regions enrichment analysis (BEHST, g:Profiler g:GOSt, GREAT, LOLA, Poly-Enrich, and ReactomePA), outlining and comparing their main features. Our comparison results indicate that the inclusion of data for regulatory elements, such as ChIP-seq, is common among these tools and could therefore improve the enrichment analysis results.
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Affiliation(s)
- Davide Chicco
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Jurman
- Data Science for Health Unit, Fondazione Bruno Kessler, Trento, Italy
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6
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Ponnusamy N, Arumugam M. Meta-analysis of active tuberculosis gene expression ascertains host directed drug targets. Front Cell Infect Microbiol 2022; 12:1010771. [PMID: 36275035 PMCID: PMC9581169 DOI: 10.3389/fcimb.2022.1010771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/21/2022] [Indexed: 12/01/2022] Open
Abstract
Multi-drug resistant tuberculosis still remains a major public health crisis globally. With the emergence of newer active tuberculosis disease, the requirement of prolonged treatment time and adherence to therapy till its completion necessitates the search of newer therapeutics, targeting human host factors. The current work utilized statistical meta-analysis of human gene transcriptomes of active pulmonary tuberculosis disease obtained from six public datasets. The meta-analysis resulted in the identification of 2038 significantly differentially expressed genes (DEGs) in the active tuberculosis disease. The gene ontology (GO) analysis revealed that these genes were major contributors in immune responses. The pathway enrichment analyses identified from various human canonical pathways are related to other infectious diseases. In addition, the comparison of the DEGs with the tuberculosis genome wide association study (GWAS) datasets revealed the presence of few genetic variants in their proximity. The analysis of protein interaction networks (human and Mycobacterium tuberculosis) and host directed drug-target interaction network led to new candidate drug targets for drug repurposing studies. The current work sheds light on host genes and pathways enriched in active tuberculosis disease and suggest potential drug repurposing targets for host-directed therapies.
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Dalgaard LT, Sørensen AE, Hardikar AA, Joglekar MV. The microRNA-29 family - role in metabolism and metabolic disease. Am J Physiol Cell Physiol 2022; 323:C367-C377. [PMID: 35704699 DOI: 10.1152/ajpcell.00051.2022] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The microRNA-29a family members miR-29a-3p, miR-29b-3p and miR-29c-3p are ubiquitously expressed and consistently increased in various tissues and cell types in conditions of metabolic disease; obesity, insulin resistance and type 2 diabetes. In pancreatic beta cells, miR-29a is required for normal exocytosis, but increased levels are associated with impaired beta cell function. Similarly, in liver miR-29 species are higher in models of insulin resistance and type 2 diabetes, and either knock-out or depletion using a microRNA inhibitor improves hepatic insulin resistance. In skeletal muscle, miR-29 upregulation is associated with insulin resistance and altered substrate oxidation, and similarly, in adipocytes over-expression of miR-29a leads to insulin resistance. Blocking miR-29a using nucleic acid antisense therapeutics show promising results in preclinical animal models of obesity and type 2 diabetes, although the widespread expression pattern of miR-29 family members complicates the exploration of single target tissues. However, in fibrotic diseases, such as in late complications of diabetes and metabolic disease (diabetic kidney disease, non-alcoholic steatohepatitis), miR-29 expression is suppressed by TGFβ allowing increased extracellular matrix collagen to form. In the clinical setting circulating levels of miR-29a and miR-29b are consistently increased in type 2 diabetes and in gestational diabetes, and are also possible prognostic markers for deterioration of glucose tolerance. In conclusion, miR-29 plays an essential role in various organs relevant to intermediary metabolism and its upregulation contribute to impaired glucose metabolism, while it suppresses fibrosis development. Thus, a correct balance of miR-29a levels seems important for cellular and organ homeostasis in metabolism.
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Affiliation(s)
- Louise T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Anja E Sørensen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Sydney, NSW, Australia
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8
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Cellular and genetic drivers of RNA editing variation in the human brain. Nat Commun 2022; 13:2997. [PMID: 35637184 PMCID: PMC9151768 DOI: 10.1038/s41467-022-30531-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/02/2022] [Indexed: 11/08/2022] Open
Abstract
Posttranscriptional adenosine-to-inosine modifications amplify the functionality of RNA molecules in the brain, yet the cellular and genetic regulation of RNA editing is poorly described. We quantify base-specific RNA editing across three major cell populations from the human prefrontal cortex: glutamatergic neurons, medial ganglionic eminence-derived GABAergic neurons, and oligodendrocytes. We identify more selective editing and hyper-editing in neurons relative to oligodendrocytes. RNA editing patterns are highly cell type-specific, with 189,229 cell type-associated sites. The cellular specificity for thousands of sites is confirmed by single nucleus RNA-sequencing. Importantly, cell type-associated sites are enriched in GTEx RNA-sequencing data, edited ~twentyfold higher than all other sites, and variation in RNA editing is largely explained by neuronal proportions in bulk brain tissue. Finally, we uncover 661,791 cis-editing quantitative trait loci across thirteen brain regions, including hundreds with cell type-associated features. These data reveal an expansive repertoire of highly regulated RNA editing sites across human brain cell types and provide a resolved atlas linking cell types to editing variation and genetic regulatory effects. Here the authors provide a deep catalogue of cell-specific A-to-I editing sites in the human cortex. Thousands of sites are enriched and elevated in neurons relative to glial cells, and are genetically regulated across multiple brain regions.
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9
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Shende N, Xu J, Li WT, Liu J, Chakladar J, Brumund KT, Ongkeko WM. Enhancer RNA Profiling in Smoking and HPV Associated HNSCC Reveals Associations to Key Oncogenes. Int J Mol Sci 2021; 22:12546. [PMID: 34830428 PMCID: PMC8625218 DOI: 10.3390/ijms222212546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/24/2021] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
Smoking and HPV infection are known causes for the vast majority of head and neck squamous cell carcinomas (HNSCC) due to their likelihood of causing gene dysregulation and genomic alterations. Enhancer RNAs (eRNAs) are non-coding RNAs that are known to increase nearby and target gene expression, and activity that has been suggested to be affected by genetic and epigenetic alterations. Here we sought to identify the effects of smoking and HPV status on eRNA expression in HNSCC tumors. We focused on four patient cohorts including smoking/HPV+, smoking/HPV-, non-smoking/HPV+, and non-smoking/HPV- patients. We used TCGA RNA-seq data from cancer tumors and adjacent normal tissue, extracted eRNA read counts, and correlated these to survival, clinical variables, immune infiltration, cancer pathways, and genomic alterations. We found a large number of differentially expressed eRNA in each patient cohort. We also found several dysregulated eRNA correlated to patient survival, clinical variables, immune pathways, and genomic alterations. Additionally, we were able to find dysregulated eRNA nearby seven key HNSCC-related oncogenes. For example, we found eRNA chr14:103272042-103272430 (eRNA-24036), which is located close to the TRAF3 gene to be differentially expressed and correlated with the pathologic N stage and immune cell populations. Using a separate validation dataset, we performed differential expression and immune infiltration analysis to validate our results from the TCGA data. Our findings may explain the association between eRNA expression, enhancer activity, and nearby gene dysregulation.
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Affiliation(s)
- Neil Shende
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jingyue Xu
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Wei Tse Li
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jeffrey Liu
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Jaideep Chakladar
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Kevin T. Brumund
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Department of Surgery, Division of Head and Neck Surgery, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Weg M. Ongkeko
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of California, San Diego, CA 92093, USA; (N.S.); (J.X.); (W.T.L.); (J.L.); (J.C.); (K.T.B.)
- Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
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10
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Sztromwasser P, Skrzypczak D, Michalak A, Fendler W. Remus: A Web Application for Prioritization of Regulatory Regions and Variants in Monogenic Diseases. Front Genet 2021; 12:638960. [PMID: 33747049 PMCID: PMC7978111 DOI: 10.3389/fgene.2021.638960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022] Open
Abstract
Background Analysis of variants in distant regulatory elements could improve the current 25–50% yield of genetic testing for monogenic diseases. However, the vast size of the regulome, great number of variants, and the difficulty in predicting their phenotypic impact make searching for pathogenic variants in the regulatory genome challenging. New tools for the identification of regulatory variants based on their relevance to the phenotype are needed. Methods We used tissue-specific regulatory loci mapped by ENCODE and FANTOM, together with miRNA–gene interactions from miRTarBase and miRWalk, to develop Remus, a web application for the identification of tissue-specific regulatory regions. Remus searches for regulatory features linked to the known disease-associated genes and filters them using activity status in the target tissues relevant for the studied disorder. For user convenience, Remus provides a web interface and facilitates in-browser filtering of variant files suitable for sensitive patient data. Results To evaluate our approach, we used a set of 146 regulatory mutations reported causative for 68 distinct monogenic disorders and a manually curated a list of tissues affected by these disorders. In 89.7% of cases, Remus identified the regulator containing the pathogenic mutation. The tissue-specific search limited the number of considered variants by 82.5% as compared to a tissue-agnostic search. Conclusion Remus facilitates the identification of regulatory regions potentially associated with a monogenic disease and can supplement classical analysis of coding variations with the aim of improving the diagnostic yield in whole-genome sequencing experiments.
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Affiliation(s)
- Paweł Sztromwasser
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Łódź, Poland
| | - Damian Skrzypczak
- Biostatistics Group, Department of Genetics, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Arkadiusz Michalak
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Łódź, Poland.,Department of Pediatrics, Diabetology, Endocrinology and Nephrology, Medical University of Lodz, Łódź, Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Łódź, Poland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
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11
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Tuvikene J, Esvald EE, Rähni A, Uustalu K, Zhuravskaya A, Avarlaid A, Makeyev EV, Timmusk T. Intronic enhancer region governs transcript-specific Bdnf expression in rodent neurons. eLife 2021; 10:65161. [PMID: 33560226 PMCID: PMC7891933 DOI: 10.7554/elife.65161] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) controls the survival, growth, and function of neurons both during the development and in the adult nervous system. Bdnf is transcribed from several distinct promoters generating transcripts with alternative 5' exons. Bdnf transcripts initiated at the first cluster of exons have been associated with the regulation of body weight and various aspects of social behavior, but the mechanisms driving the expression of these transcripts have remained poorly understood. Here, we identify an evolutionarily conserved intronic enhancer region inside the Bdnf gene that regulates both basal and stimulus-dependent expression of the Bdnf transcripts starting from the first cluster of 5' exons in mouse and rat neurons. We further uncover a functional E-box element in the enhancer region, linking the expression of Bdnf and various pro-neural basic helix–loop–helix transcription factors. Collectively, our results shed new light on the cell-type- and stimulus-specific regulation of the important neurotrophic factor BDNF.
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Affiliation(s)
- Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
| | - Eli-Eelika Esvald
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
| | - Annika Rähni
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kaie Uustalu
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, United Kingdom
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia.,Protobios LLC, Tallinn, Estonia
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12
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Wu M, Karadoulama E, Lloret-Llinares M, Rouviere JO, Vaagensø CS, Moravec M, Li B, Wang J, Wu G, Gockert M, Pelechano V, Jensen TH, Sandelin A. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res 2020; 48:8509-8528. [PMID: 32710631 PMCID: PMC7470964 DOI: 10.1093/nar/gkaa594] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.
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Affiliation(s)
- Mengjun Wu
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Evdoxia Karadoulama
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Marta Lloret-Llinares
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.,European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jerome Olivier Rouviere
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Christian Skov Vaagensø
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Martin Moravec
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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13
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Association between brown eye colour in rs12913832:GG individuals and SNPs in TYR, TYRP1, and SLC24A4. PLoS One 2020; 15:e0239131. [PMID: 32915910 PMCID: PMC7485777 DOI: 10.1371/journal.pone.0239131] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809.
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14
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Macedo A, Gontijo AM. The intersectional genetics landscape for humans. Gigascience 2020; 9:giaa083. [PMID: 32761099 PMCID: PMC7407247 DOI: 10.1093/gigascience/giaa083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/05/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The human body is made up of hundreds-perhaps thousands-of cell types and states, most of which are currently inaccessible genetically. Intersectional genetic approaches can increase the number of genetically accessible cells, but the scope and safety of these approaches have not been systematically assessed. A typical intersectional method acts like an "AND" logic gate by converting the input of 2 or more active, yet unspecific, regulatory elements (REs) into a single cell type specific synthetic output. RESULTS Here, we systematically assessed the intersectional genetics landscape of the human genome using a subset of cells from a large RE usage atlas (Functional ANnoTation Of the Mammalian genome 5 consortium, FANTOM5) obtained by cap analysis of gene expression sequencing (CAGE-seq). We developed the heuristics and algorithms to retrieve and quality-rank "AND" gate intersections. Of the 154 primary cell types surveyed, >90% can be distinguished from each other with as few as 3 to 4 active REs, with quantifiable safety and robustness. We call these minimal intersections of active REs with cell-type diagnostic potential "versatile entry codes" (VEnCodes). Each of the 158 cancer cell types surveyed could also be distinguished from the healthy primary cell types with small VEnCodes, most of which were robust to intra- and interindividual variation. Methods for the cross-validation of CAGE-seq-derived VEnCodes and for the extraction of VEnCodes from pooled single-cell sequencing data are also presented. CONCLUSIONS Our work provides a systematic view of the intersectional genetics landscape in humans and demonstrates the potential of these approaches for future gene delivery technologies.
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Affiliation(s)
- Andre Macedo
- Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150–190, Lisbon, Portugal
| | - Alisson M Gontijo
- Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua do Instituto Bacteriológico 5, 1150–190, Lisbon, Portugal
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15
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Di Giorgio E, Dalla E, Franforte E, Paluvai H, Minisini M, Trevisanut M, Picco R, Brancolini C. Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells. Nucleic Acids Res 2020; 48:646-664. [PMID: 31754707 PMCID: PMC6954409 DOI: 10.1093/nar/gkz1120] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/28/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
Transcriptional networks supervising class IIa HDAC expression are poorly defined. Here we demonstrate that MEF2D is the key factor controlling HDAC9 transcription. This control, which is part of a negative feed-back loop during muscle differentiation, is hijacked in cancer. In leiomyosarcomas the MEF2D/HDAC9 vicious circuit sustains proliferation and cell survival, through the repression of the death receptor FAS. Comprehensive genome-wide studies demonstrate that HDAC4 and HDAC9 control different genetic programs and show both specific and common genomic binding sites. Although the number of MEF2-target genes commonly regulated is similar, only HDAC4 represses many additional genes that are not MEF2D targets. As expected, HDAC4-/- and HDAC9-/- cells increase H3K27ac levels around the TSS of the respective repressed genes. However, these genes rarely show binding of the HDACs at their promoters. Frequently HDAC4 and HDAC9 bind intergenic regions. We demonstrate that these regions, recognized by MEF2D/HDAC4/HDAC9 repressive complexes, show the features of active enhancers. In these regions HDAC4 and HDAC9 can differentially influence H3K27 acetylation. Our studies describe new layers of class IIa HDACs regulation, including a dominant positional effect, and can contribute to explain the pleiotropic actions of MEF2 TFs.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | | | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Matteo Trevisanut
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Raffaella Picco
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy
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16
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Rydbirk R, Folke J, Busato F, Roché E, Chauhan AS, Løkkegaard A, Hejl AM, Bode M, Blaabjerg M, Møller M, Danielsen EH, Brudek T, Pakkenberg B, Tost J, Aznar S. Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients. Acta Neuropathol Commun 2020; 8:29. [PMID: 32151281 PMCID: PMC7063795 DOI: 10.1186/s40478-020-00908-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 02/06/2023] Open
Abstract
Multiple system atrophy (MSA) is a rare disease with a fatal outcome. To date, little is known about the molecular processes underlying disease development. Its clinical overlap with related neurodegenerative movement disorders underlines the importance for expanding the knowledge of pathological brain processes in MSA patients to improve distinction from similar diseases. In the current study, we investigated DNA methylation changes in brain samples from 41 MSA patients and 37 healthy controls. We focused on the prefrontal cortex, a moderately affected area in MSA. Using Illumina MethylationEPIC arrays, we investigated 5-methylcytosine (5mC) as well as 5-hydroxymethylcytosine (5hmC) changes throughout the genome. We identified five significantly different 5mC probes (adj. P < 0.05), of which one probe mapping to the AREL1 gene involved in antigen presentation was decreased in MSA patients. This decrease correlated with increased 5hmC levels. Further, we identified functional DNA methylation modules involved in inflammatory processes. As expected, the decreased 5mC levels on AREL1 was concordant with increased gene expression levels of both AREL1 as well as MHC Class I HLA genes in MSA brains. We also investigated whether these changes in antigen-related processes in the brain associated with changes in peripheral mononuclear cells. Using flow cytometry on an independent cohort of MSA patients, we identified a decrease in circulating non-classical CD14+CD16++ blood monocytes, whereas T and NK cell populations were unchanged. Taken together, our results support the view of an active neuroimmune response in brains of MSA patients.
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17
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Whole genome and transcriptome sequencing of post-mortem cardiac tissues from sudden cardiac death victims identifies a gene regulatory variant in NEXN. Int J Legal Med 2019; 133:1699-1709. [PMID: 31392414 DOI: 10.1007/s00414-019-02127-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sudden cardiac death (SCD) is a major public health problem and constitutes a diagnostic and preventive challenge in forensic pathology, especially for cases with structural normal hearts at autopsy, so-called sudden arrhythmic death syndrome (SADS). The identification of new genetic risk factors that predispose to SADS is important, because they may contribute to establish the diagnosis and increase the understanding of disease pathways underlying SADS. Pathogenic mutations in the protein coding regions of cardiac genes were found in relation to SADS. However, much remains unknown about variants in non-coding regions of the genome. METHODS AND RESULTS In this study, we explored the potential of whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) to find DNA variants in SCD victims with structural normal hearts. With focus on the non-coding regulatory regions, we re-examined a cohort of 13 SADS and sudden unexplained death in infancy (SUDI) victims without disease causing DNA variants in recognized cardiac genes. The genetic re-examination of DNA was carried out using frozen tissue samples and WTS was carried out using five distinct formalin fixed and paraffin embedded (FFPE) cardiac tissue samples from each individual, including anterior and posterior walls of the left ventricle, ventricular papillary muscle, septum, and the right ventricle. We identified 23 candidate variants in regulatory sequences of cardiac genes, including a variant in the promotor region of NEXN, c.-194A>G, that was found to be statistically significantly (p < 0.05) associated with decreased expression of NEXN and cardiac hypertrophy. CONCLUSION With the use of post-mortem FFPE tissues, we highlight the potential of using WTS investigations and compare gene expression levels with DNA variation in regulatory non-coding regions of the genome for a better understanding of the genetics of cardiac diseases leading to SCD.
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18
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Palmieri V, Backes C, Ludwig N, Fehlmann T, Kern F, Meese E, Keller A. IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions. Nucleic Acids Res 2019; 46:D770-D775. [PMID: 28977416 PMCID: PMC5753248 DOI: 10.1093/nar/gkx701] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/28/2017] [Indexed: 12/12/2022] Open
Abstract
Web repositories for almost all 'omics' types have been generated-detailing the repertoire of representatives across different tissues or cell types. A logical next step is the combination of these valuable sources. With IMOTA (interactive multi omics tissue atlas), we developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between mRNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens. IMOTA also contains data on tissue-specific interactions, e.g. information on 331 413 miRNAs and target gene pairs that are jointly expressed in the considered tissues. By using intuitive filter and visualization techniques, it is with minimal effort possible to answer various questions. These include rather general questions but also requests specific for genes, miRNAs or proteins. An example for a general task could be 'identify all miRNAs, genes and proteins in the lung that are highly expressed and where experimental evidence proves that the miRNAs target the genes'. An example for a specific request for a gene and a miRNA could for example be 'In which tissues is miR-34c and its target gene BCL2 expressed?'. The IMOTA repository is freely available online at https://ccb-web.cs.uni-saarland.de/imota/.
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Affiliation(s)
- Valeria Palmieri
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department for Human Genetics, Saarland University, 66424 Homburg, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department for Human Genetics, Saarland University, 66424 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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Daniel S, Nylander V, Ingerslev LR, Zhong L, Fabre O, Clifford B, Johnston K, Cohn RJ, Barres R, Simar D. T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors. Clin Epigenetics 2018; 10:138. [PMID: 30400990 PMCID: PMC6219017 DOI: 10.1186/s13148-018-0561-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 10/07/2018] [Indexed: 01/08/2023] Open
Abstract
Background Cancer treatments have substantially improved childhood cancer survival but are accompanied by long-term complications, notably chronic inflammatory diseases. We hypothesize that cancer treatments could lead to long-term epigenetic changes in immune cells, resulting in increased prevalence of inflammatory diseases in cancer survivors. Results To test this hypothesis, we established the epigenetic and transcriptomic profiles of immune cells from 44 childhood cancer survivors (CCS, > 16 years old) on full remission (> 5 years) who had received chemotherapy alone or in combination with total body irradiation (TBI) and hematopoietic stem cell transplant (HSCT). We found that more than 10 years post-treatment, CCS treated with TBI/HSCT showed an altered DNA methylation signature in T cell, particularly at genes controlling immune and inflammatory processes and oxidative stress. DNA methylation remodeling in T cell was partially associated with chronic expression changes of nearby genes, increased frequency of type 1 cytokine-producing T cell, elevated systemic levels of these cytokines, and over-activation of related signaling pathways. Survivors exposed to TBI/HSCT were further characterized by an Epigenetic-Aging-Signature of T cell consistent with accelerated epigenetic aging. To investigate the potential contribution of irradiation to these changes, we established two cell culture models. We identified that radiation partially recapitulated the immune changes observed in survivors through a bystander effect that could be mediated by circulating factors. Conclusion Cancer treatments, in particular TBI/HSCT, are associated with long-term immune disturbances. We propose that epigenetic remodeling of immune cells following cancer therapy augments inflammatory- and age-related diseases, including metabolic complications, in childhood cancer survivors. Electronic supplementary material The online version of this article (10.1186/s13148-018-0561-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Daniel
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Vibe Nylander
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, Australia
| | - Odile Fabre
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Briana Clifford
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Karen Johnston
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Richard J Cohn
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Romain Barres
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
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Monitoring transcription initiation activities in rat and dog. Sci Data 2017; 4:170173. [PMID: 29182598 PMCID: PMC5704677 DOI: 10.1038/sdata.2017.173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 10/04/2017] [Indexed: 12/27/2022] Open
Abstract
The promoter landscape of several non-human model organisms is far from complete. As a part of FANTOM5 data collection, we generated 13 profiles of transcription initiation activities in dog and rat aortic smooth muscle cells, mesenchymal stem cells and hepatocytes by employing CAGE (Cap Analysis of Gene Expression) technology combined with single molecule sequencing. Our analyses show that the CAGE profiles recapitulate known transcription start sites (TSSs) consistently, in addition to uncover novel TSSs. Our dataset can be thus used with high confidence to support gene annotation in dog and rat species. We identified 28,497 and 23,147 CAGE peaks, or promoter regions, for rat and dog respectively, and associated them to known genes. This approach could be seen as a standard method for improvement of existing gene models, as well as discovery of novel genes. Given that the FANTOM5 data collection includes dog and rat matched cell types in human and mouse as well, this data would also be useful for cross-species studies.
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